|
| Status |
Public on Apr 25, 2013 |
| Title |
252035310005_1_3-T5[D(5)/D(3)] |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
T5_D
|
| Organism |
Naumovozyma castellii |
| Characteristics |
treatment: hydrogen peroxide
time point (minutes): 5
|
| Treatment protocol |
Salt Stress: Cultures were grown to mid-log densities (between 5x10^7 and 1x10^8 cells/mL) at 30C and treated with hydrogen peroxide to a final concentration of 5 mM. Samples were harvested at different time intervals (5, 15, 30, 60 minutes after treatment)
|
| Growth protocol |
Cells were plated onto BMW plates from frozen glycerol stocks. After 2 days, cells were taken from plates and grown overnight in BMW medium at 30 ° C in a New Brunswick Scientific Edison model TC-7 roller drum on the highest speed until saturated (1-2 days). These saturated cultures were then used to inoculate 300 ml BMW batch cultures in 2 liter Erlenmeyer flasks at 1 x 106 cells/mL for the glucose depletion and repletion experiments described below. Flasks were transferred to New Brunswick Scientific Edison water bath model C76 shakers set to 200 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Yeast RNA extraction
|
| Label |
Cy5
|
| Label protocol |
Total RNA samples were reverse transcribed to cDNA and labeled with either Cy3 or Cy5 using a modification of the protocol developed by Joe Derisi (UCSF) and Rosetta Inpharmatics (Kirkland, WA) that can be obtained at www.microarrays.com.
|
| |
|
| Channel 2 |
| Source name |
T0_D
|
| Organism |
Naumovozyma castellii |
| Characteristics |
time point (minutes): 0
|
| Treatment protocol |
Salt Stress: Cultures were grown to mid-log densities (between 5x10^7 and 1x10^8 cells/mL) at 30C and treated with hydrogen peroxide to a final concentration of 5 mM. Samples were harvested at different time intervals (5, 15, 30, 60 minutes after treatment)
|
| Growth protocol |
Cells were plated onto BMW plates from frozen glycerol stocks. After 2 days, cells were taken from plates and grown overnight in BMW medium at 30 ° C in a New Brunswick Scientific Edison model TC-7 roller drum on the highest speed until saturated (1-2 days). These saturated cultures were then used to inoculate 300 ml BMW batch cultures in 2 liter Erlenmeyer flasks at 1 x 106 cells/mL for the glucose depletion and repletion experiments described below. Flasks were transferred to New Brunswick Scientific Edison water bath model C76 shakers set to 200 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Yeast RNA extraction
|
| Label |
Cy3
|
| Label protocol |
Total RNA samples were reverse transcribed to cDNA and labeled with either Cy3 or Cy5 using a modification of the protocol developed by Joe Derisi (UCSF) and Rosetta Inpharmatics (Kirkland, WA) that can be obtained at www.microarrays.com.
|
| |
|
| |
| Hybridization protocol |
Standard Agilent protocols for Agilent 8x15K and 4x44K Oligo Microarrays
|
| Scan protocol |
Arrays were scanned using an Agilent scanner and analyzed with Agilent’s feature extraction software version 10.5.1.1.
|
| Description |
Biological replicate D, technical replicate 1
|
| Data processing |
Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization. Reported expression values for each gene are median log2 ratios across all probes.
|
| |
|
| Submission date |
May 31, 2012 |
| Last update date |
Apr 25, 2013 |
| Contact name |
Ilan Wapinski |
| E-mail(s) |
ilan@broadinstitute.org
|
| Organization name |
Broad Institute
|
| Lab |
Aviv Regev
|
| Street address |
7 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02140 |
| Country |
USA |
| |
|
| Platform ID |
GPL10501 |
| Series (1) |
| GSE38478 |
Evolutionary principles of modular gene regulation in Yeasts |
|
